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MAGNET: Multi-view graph autoencoder with cell-gene attention for cell interaction network reconstruction from spatial transcriptomics

Fig 5

Hyperparameter sensitivity analysis of MAGNET.

(A–D) Effects of , , τ, and m on average precision (AP). (E–F) Quantitative summaries showing the variation range (<1) and corresponding p-values for each parameter, all remaining above 0.05, indicating no statistically significant difference across settings. (G) Evaluation of the neighborhood size k (the number of nearest neighboring cells) in graph construction across spatial, ligand–receptor, and transcriptional graphs. MAGNET maintains stable AP, ROC-AUC, and F1 scores when k varies from 3 to 10, confirming robustness to local connectivity settings.

doi: https://doi.org/10.1371/journal.pcbi.1013810.g005